title: M-Cd36 fl/fl , replicates pool 4x, scRNAseq

status: Public on May 31 2024

type: SRA

city: New York City

first: Dimitris

last: Nasias

state: New York

address: 550 1st Avenue

department: Langone Medical School

country: USA

institute: New York University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: peritoneum

extract_protocol:
Freshly collected murine peritoneal cells mice with ice-cold 1x PBS. Cells were processed for single cell RNA Sequencing according to 10x standard protocol.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up, amplified by PCR and the apropiated sized fragments were selected for subsequent library construction.

treatment_protocol: Macrophage-Cd36-/- and macrophage-Cd36 fl/fl mice were administered  high dosage of zymosan (1mg/ animal) in the peritoneal cavity and total peritoneal cells were collected from euthanized animals 3 days after.

tag: cell type

value: peritoneal cells

tag: tissue

value: peritoneum

tag: strain

value: floxed CD36

tag: age

value: 10-14 weeks old


title: M-Cd36-/- , replicates pool 4x, scRNAseq

description: 10x Genomics

value: LysM-Cre (x) floxed CD36


title: YTK558-1-H3

city: Chuncheon

first: Junsoo

last: Oh

country: South Korea

institute: Kangwon National University

library_source: genomic

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombe spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast cell

growth_protocol: All strains were grown in 200ml of YPD (Yeast extract Peptone Dextrose; 1% Yeast Extract, 2% Peptone, 2% Dextrose (Glucose)) at 30℃ until OD600 was 0.5-0.6

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift BioSciences, 21096) following the manufacture’s instruction.

value: Yeast cell

tag: chip antibody

value: Anti-Histone H3 (Abcam, ab1791)

tag: genotype

value: shg1 spp1 double deletion


title: YTK558-2-H3


title: YTK558-2-H3K4me2

value: Anti-dimethyl-Histone H3 (Lys4) (Merck, 07-030)


title: YTK558-1-H3K4me2


title: YTK556-2-H3

value: spp1 deletion


title: YTK558-2-H3K4me3

value: Anti-trimethyl-Histone H3 (Lys4) (Merck, 07-473)


title: YTK556-1-H3


title: YTK556-2-H3K4me2


title: YTK556-1-H3K4me2


title: YTK556-2-H3K4me3


title: YTK556-1-H3K4me3


title: YTK482-2-H3

value: shg1 deletion


title: YTK482-1-H3


title: YTK482-2-H3K4me2


title: T2DMgroup_2

city: Qingdao

first: Kuishuai

last: Xu

state: --- Select One ---

country: China

institute: the affiliated hospital of qingdao university

library_source: transcriptomic

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Gastrocnemius muscle

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastrocnemius muscle


title: YTK482-1-H3K4me2


title: T2DMgroup_1


title: T2DMgroup_3


title: YTK482-2-H3K4me3


title: YTK482-1-H3K4me3


title: YF336-2-H3

value: Wildtype (BY4741)


title: YTK558-1-H3K4me3


title: Controlgroup_2


title: YF336-1-H3


title: Controlgroup_1


title: YF336-1-H3K4me2


title: YF336-2-H3K4me3


title: YF336-1-H3K4me3


title: ami-UPP-4 knockdown at control condition rep 3

city: Kaiserslautern

first: Torsten

last: Möhlmann

address: Paul-Ehrlich-Str

department: Biology

country: Germany

institute: University of Kaiserslautern

description:
R4_22 biol rep 3
R4_3_22

data_processing:
The data processing steps are according to Novogene methods: Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignment: Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome. In general, HISAT2 supports genomes of any size, including those larger than 4 billion bases and most of the parameters are set to default. Spliced reads of RNA Seq data can be effictively aligned using HISAT2. HISAT2 v2.0.5 was run using the --dta --phred33 parameters.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: plants were grown for 4-5 weeks under short days (10h light/14h dark) at 120 mE, 65% relative humidity, 21°C in standard soil substrate

extract_protocol:
RNA was extracted from leaves or leaf discs using the NucleoSpin® RNA Plant Kit (Macherey-Nagel) according to the manufacturer's instructions. 50 mg of fresh plant material was used for this purpose. The RNA was eluted from the column with 40 μl of RNase-free ddH2O
Library construction was perfomed by Novogene Sequencing Service. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection
RNASeq library of poly-A enriched transcripts

treatment_protocol: Samples of  Col-0 (wild-type control) plants and ami-UPP knock down plants  were harvested either after 3 hours of light (ML, control) or after three hours of high light (HL) at 1000μmol in three biological replicates.

value: leaf

tag: cell line

value: mesophyll cell

value: knock down

tag: treatment


title: control plants HL rep 3

description:
Col_0_HL biol rep 3
Col_0_3_HL

value: wild type

value: high light


title: ami-UPP-4 knockdown HL rep 1

description:
R4_HL biol rep 1
R4_1_HL


title: ami-UPP-4 knockdown HL rep 3

description:
R4_HL biol rep 3
R4_3_HL


title: ami-UPP-4 knockdown at control condition rep 2

description:
R4_22 biol rep 2
R4_2_22


title: ami-UPP-4 knockdown HL rep 2

description:
R4_HL biol rep 2
R4_2_HL


title: control plants HL rep 2

description:
Col_0_HL biol rep 2
Col_0_2_HL


title: Controlgroup_3


title: WT_CB_5day_rep3

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

data_processing:
Basecalls performed using Illumina CASAVA1.7 software.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene.
Differential expression analysis oftwo conditions/groups (two biological replicates per condition) was performedusing the DESeq2 R package (1.20.0).
Assembly: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/280/675/GCF_000280675.1_ASM28067v1/GCF_000280675.1_ASM28067v1_genomic.fna.gz
Supplementary files format and content: The data was filed with FPKM of each detected genes and formed excel file.

organism: Beauveria bassiana

source_name: strain

growth_protocol: Aliquots of 50 mL 10^6 conidia/mL cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton were incubated by shaking at 150 rpm for 5 days at 25 ℃.

extract_protocol:
After 5-day CB incubation, total RNA was extracted from three replicating cultures of Ngs1-deletion mutants and wild-type strain under the action of an RNAisoTM Plus Reagent (TaKaRa, Dalian, China), respectively.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out usingdivalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragmentsof preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers andIndex (X) Primer. At last, PCR products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: No specific treatment for each strain.

value: strain

value: hyphal body

value: Cultivated in cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 ℃.


title: Ngs1_CB_5day_rep3

value: Ngs3 deletion


title: ami-UPP-4 knockdown at control condition rep 1

description:
R4_22 biol rep 1
R4_1_22


title: WT_CB_5day_rep2


title: Ngs1_CB_5day_rep2

value: Ngs2 deletion


title: control plants at control condition rep 2

description:
Col_0_22 biol rep 2
Col_0_2_22


title: control plants at control condition rep 1

description:
Col_0_22 biol rep 1
Col_0_1_22


title: Ngs1_CB_5day_rep1

value: Ngs1 deletion


title: YF336-2-H3K4me2

value: Yeast cell

value: Anti-dimethyl-Histone H3 (Lys4) (Merck, 07-030)


title: RB3823_S5_L001_doxy_negative_biological_replicate3

city: Essen

first: Petra

last: Ketteler

address: Hufelandstraße 55

institute: University Hospital Essen

description:
MYCN knockdown model
ryl_et_al_MYCNKD_sleuth.txt

data_processing:
Assembly: hg38
Illumina bcl2fastq (2.20) was used to demultiplex the sequenced reads
For paired end sequencing, adapter trimming was performed with skewer (version 0.2.2) (Jiang et al. 2014)
For single read sequencing, adapter trimming was performed automatically with cutadapt
Sample specific fastq files were aligned to the reference transcriptome (GRCh38) by kallisto running 100 bootstraps
Differential gene expression analysis was performed with sleuth
Expression values were exported from the sleuth object as normalized TPM values
Supplementary files format and content: tab-delimited text file includes log2-transformed TPM+1 values for each sample from 52 retinoblastoma patients
Supplementary files format and content: tab-delimited text file includes log2-transformed TPM+1 values for each sample from 8 retinoblastoma cell lines
Supplementary files format and content: tab-delimited text file containing Arriba output
Supplementary files format and content: tab-delimited text file containing output of Wald test (sleuth) for significant differences between MYCNKD_doxy_positive vs MYCNKD_doxy_negative cells

organism: Homo sapiens

source_name: retinoblastoma

extract_protocol:
Total RNA from primary tumor samples was isolated using the RNeasy Mini Kit (Qiagen) or Monarch Total RNA Miniprep kit (New England Biolabs GmbH) Total RNA from retinoblastoma cells was isolated using Rneasy mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer's protocols.

value: retinoblastoma

value: MYCNKD

tag: rb1 status

tag: mycn amplification

value: control


title: RB3823_S4_L001_doxy_positive_biological_replicate2

value: doxycycline


title: RB3823_S3_L001_doxy_negative_biological_replicate2


title: control plants HL rep 1

description:
Col_0_HL biol rep 1
Col_0_1_HL

value: leaf


title: 8-AG treated Fisher344 rat retina-03

city: Pittsburgh

first: Yuanyuan

last: Chen

state: PA

address: 1622 Locust Street,

department: Ophthalmology

institute: University of Pittsburgh

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
gene expression level was estimated using RSEM v1.2.15
Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p<0.05 and more than 1.5 fold changes were considered differentially expressed.
Goseq was used to perform GO enrichment analysis and Kobas was used to perform the pathway analysis.
Assembly: Rnor_6.0
Supplementary files format and content: txt and csv files include raw counts of each sample.
Supplementary files format and content: txt and csv files include RPKM values of each sample.
Supplementary files format and content: txt and csv files include fold change, p values, FDR and RPKM values of each sample in two groups
Supplementary files format and content: excel files include the DEGs upreguated and downregulated between two groups.

source_name: neural retina

growth_protocol: We obtained young and aged Fischer 344 rats from Char les River Laboratories and the National Institute on Aging [NIA]. All animals were housed under standard 12-h light/12-h dark conditions in the animal facility at University of Pittsburgh.

extract_protocol:
Each eye ball was opened by removing the cornea, iris and lens, and the neural retina was firstly isolated and put into RNAzol immediately and flash frozen in liquid nitrogen. After the neural retina being taken, RPE/choroids were isolated by washing the remaining eye cup with RNA zol and flash frozed in liquid nitrogen. Total RNA was isolated follwing manufacturer's instructions of RNAzol (Sigma-Aldrich, Saint-Louis, MO). Only samples with RNA integrity number (RIN) > 7 was selected for poly-A captured mRNA library preparation.
To compare old vs. young and 8-AG treated aged vs untreated aged neural retinae, mRNA libraries were prepared using poly-A capturation (N=3).  For RNA from RPE/choroids, due to low RNA yield,  mRNA lirbaries were genereated using polyA selection with enrichment for full-length transcripts.

treatment_protocol: We used four months adult rats as young control and aged rats at 22-24 months of age with or without 8-AG treatment. The 22 months old rats were treated with 8-AG (5 mg/kg body weight per day) daily by supplementing 8-AG in drinking water or water only for the untreated old group. Animals were treated for 8 weeks until they were 24 months of age and they were euthanized and eyes were enucleated immediately.

value: neural retina

value: WT

value: 8-AG treated old-24 months


title: 8-AG treated Fisher344 rat retina-01


title: Aged Fischer344 rat retina-03

molecule: polyA RNA

value: untreated old-24 months


title: RB3823_S6_L001_doxy_positive_biological_replicate3


title: 8-AG treated Fisher344 rat retina-02


title: RB3823_S1_L001_doxy_negative_biological_replicate1


title: WT_CB_5day_rep1

value: strain

value: wild type


title: RB3823_S2_L001_doxy_positive_biological_replicate1


title: Aged Fischer344 rat retina-01


title: 8h_Mock_REP2

city: Cologne

first: Miltos

last: Tsiantis

state: North Rhine-Westphalia

address: Carl-von-Linné-Weg, 10

department: Department of Comparative Development and Genetics

institute: Max Planck Institue for Plant Breeding Research

data_processing:
Single-end reads were aligned to the C. hirsuta reference genome (CHIV1, http://chi.mpipz.mpg.de/) using STAR v2.4.2a with default parameters.
Raw read counts per gene were quantified with HTSeq v0.5.4p1 (https://www-huber.embl.de/users/anders/HTSeq/) using the “--stranded=no --type=CDS’’ option.
Differential expressed genes between the Dexamethasone-treated and Mock-treated samples were determined using DESeq (Anders and Huber, 2010).
We found the most sensitive parameter settings for the function estimateDispersions were method= “blind”, and sharingMode= “fitonly”  (Mott et al., 2014).
Gene ontology (GO) analysis of ChCUC1 downstream responsive genes was performed by converting the C. hirsuta gene IDs into their A. thaliana orthologue gene IDs, followed by analysis by enrichGO function in the ClusterProfiler package (Yu et al., 2012) in R.
Assembly: carhr38
Supplementary files format and content: Tab-delimited files includes raw counts for each sample
Supplementary files format and content: Tab-delimited files includes raw counts for each replicate

organism: Cardamine hirsuta

source_name: shoot apices

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen 74904). DNase I treatment was conducted on-column during the RNA extraction by RNase-Free DNase Set (Qiagen 79254).
1µg of total RNA was used for library preparation following polyA mRNA workflow using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760L)

value: shoot apices

tag: time point

value: Oxford

value: Mock


title: Young Fischer344 rat retina-03

value: untreated young-4 months


title: 8h_Dex_REP3

value: Dex


title: 8h_Mock_REP3


title: control plants at control condition rep 3

description:
Col_0_22 biol rep 3
Col_0_3_22

value: mesophyll cell


title: Aged Fischer344 rat retina-02


title: Young Fischer344 rat retina-01


title: 8h_Dex_REP2


title: Young Fischer344 rat retina-02


title: 8h_Dex_REP1


title: 6h_Dex_REP3


title: 6h_Dex_REP2


title: 6h_Dex_REP1


title: Hi-c data for wildtype LNCaP repeat1

city: La Jolla

first: Amir

last: Gamliel

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

data_processing:
Hi-C data were procced using Juicer (version 1.6.2) to generate .hic files.
Assembly: hg19
Supplementary files format and content: .hic files were generated by juicertools with default parameters.

source_name: Prostate

growth_protocol: LNCaP cells were growing in IMDM medium with  with 10% FBS and 5% CO2 at 37°C incubator.

extract_protocol:
Cells were extracted in 200 µl 0.5% SDS, 50 mM Tris/HCl, pH 7.5, 10 mM NaCL, 1mM EDTA and 1x Roche complete.
libraries were prepared using the KAPA HTP/LTP Library Preparation Kits

treatment_protocol: 5 million LNCaP cells in 10cm plates were fixed for 10 minutes  at room temperature with 5ml of  1% Formaldehyde in PBS, then quenched with 660 µl 2.625 M glycine with10% BSA , washed once with 1 ml 0.5% BSA/PBS in 1.5 ml Eppendorf tube and once with 200 µl 0.5% BSA/PBS in tube strip

value: Prostate

value: LNCaP

value: Cancer cell

value: no


title: Hi-c data for wildtype LNCaP repeat2


title: Hi-c data for ERG gene nearby TAD boundary deteletion LNCaP repeat1

value: TAD Boundary deletion


title: 8h_Mock_REP1


title: 4h_Mock_REP2


title: Hi-c data for ERG gene nearby TAD boundary deteletion LNCaP repeat2


title: cut100, K562 cells

city: Xiamen

first: Xing

address: 422, Siming South Road

institute: Xiamen University

data_processing:
Trim_galore version 0.6.10 was utilized for initial sequence quality control and adapter sequence removal, applying parameters: -q 25 --phred33 --length 25 -e 0.1 --stringency 4.
Bowtie2 version 2.2.9 aligned the quality-trimmed paired-end sequencing data to reference genomes (GRCh38 for human and GRCm38 for mouse), using parameters: -p 10 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Mitochondrial genes were excluded during alignment. Data were randomly downsampled to the desired depth for analysis. MACS2 version 2.2.6 executed peak calling with parameters: callpeak -g hs -p 1e-5 -f BEDPE --keep-dup all.
Peaks intersecting ENCODE blacklisted regions were excluded for both human and mouse analyses. For mES cells analysis, we capitalized on the low-input characteristic of DMF-ChIP-seq and proceeded with only 1M reads.
Assembly: hg38
Supplementary files format and content: Signal peak annotation bigwig file in bw file
Library strategy: CUT&Tag

source_name: marrow

growth_protocol: K562 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin. HeLa cells were cultured in Minimum Essential medium supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin. mES cells were cultured on 0.1% Gelatin pretreated culture flask and in Dulbecco’s modified Eagle medium supplemented with 15% Fetal Bovine Serum, 2 mM L-glutamine, 0.1mM Non-Essential Amino Acids, 0.1 mM 2-mercaptoethnol, and 1000U/mL recombinant leukemia inhibitory factor.

extract_protocol:
The DNAs of cells were released and enriched by using DNA extraction buffer (6 μL Buffer L/B, 0.3 μL Proteinase K, 1.2 μL DNA Extract Beads and 0.375 μL 1% F68)
DNA libraries were constructed according to CUT&Tag.

treatment_protocol: Recombinant leukemia inhibitory factor was withdrawn from medium for mES cells differentiation.

value: marrow

value: marrow cancer cells


title: cut99, K562 cells

value: WT


title: cut33, K562 cells


title: cut105, HeLa cells

source_name: uterus

value: uterus

value: HeLa

value: uterus cancer cells


title: cut106, HeLa cells


title: cut110, HeLa cells


title: cut93, K562 cells


title: cut109, HeLa cells


title: cut108, HeLa cells


title: 4h_Mock_REP1

value: shoot apices


title: cut107, HeLa cells


title: 2h_Mock_REP3

value: Oxford


title: 6h_Mock_REP2

value: Mock


title: cut102, K562 cells


title: 2h_Mock_REP2


title: cut104, K562 cells


title: 2h_Mock_REP1


title: 6h_Mock_REP1


title: 4h_Mock_REP3


title: 6h_Mock_REP3


title: cut103, K562 cells


title: 2h_Dex_REP3


title: cut54, K562 cells


title: 4h_Dex_REP3


title: 2h_Dex_REP2


title: cut22, K562 cells


title: 2h_Dex_REP1


title: 4h_Dex_REP1


title: cut53, K562 cells


title: cut17, K562 cells


title: cut29, K562 cells


title: 4h_Dex_REP2


title: Input for ChIP-seq on Cord Blood HSPC

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

data_processing:
Alignment: Bowtie2 v2.2.5
Coverage file: Bedcovering, Deep tools
Assembly: hg19
Supplementary files format and content: bigWig tracks for each of the samples.

source_name: Cord blood

growth_protocol: Cord Blood is mechanically disrupted. CD34+ cells are magnetically separated and infected with MLLT3_OE lentivirus or control and cultured for 8 days in StemspanII.

extract_protocol:
Cells are crosslinked 10' in 1% formaldehide, lysed and sonicated. The indicated mark is immunoprecipitated overnight, and enriched by magnetic isolation. IP fraction is eluted and DE crosslinked.
Ovation Ultralow v2 (Nugent).

treatment_protocol: Lentivirus infection with MLLT3 overexpression or empty vector.

value: Cord blood

value: HSPC

value: CTR OE

tag: antibody


title: 25-9-RNA-R2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Raw ChIP-seq reads were aligned to hg19 genome by bwa (0.7.17).
Aligned reads were deduplicated and those with MAPQ>=10 were retained.
Narrow peaks (H3K27ac, H3K4me1, H3K4me3) were called by MACS2 (2.2.7.1) with q-value<=0.05. Board peaks (H3K27me3, H3K9me3) were called by Homer findPeaks in histone mode with p-value<=0.05.
Raw RNA-seq reads were trimmed by Trim Galore.
Trimmed RNA-seq reads were aligned to hg19 genome by STAR.
Assembly: hg19
Supplementary files format and content: bigwig track files (ChIP-seq)
Supplementary files format and content: txt gene read count files (RNA-seq)

source_name: Lung

extract_protocol:
Nuclei extraction: Samples were shipped to Virginia Tech on dry ice and stored in liquid nitrogen vapor phase until use. Thin slices were cut from the tissue on dry ice with a sharp scalpel and transferred to the grinder (D9063, Sigma-Aldrich) pre-cooled on ice. Subsequent steps were performed on ice and centrifugation performed at 4°C. 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use] was added to the grinder. Tissue was homogenized by slowly douncing 20 times with pestle A and 30 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. Supernatant was removed and the crude nuclei pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by gently pipetting and then inverting the tube five times. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. The purified nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS).  MNase digestion of chromatin: Resuspended nuclei were counted and diluted to 4×10^6/ml if needed. 2 µl of PIC, 2 µl of 100 mM PMSF and 200 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added to 200 µl of nuclei suspension, mixed by vortexing and incubated at room temperature for 10 min. 20 µl of 100 mM CaCl2 and 5 µl of 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 44 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing chromatin fragments were transferred to a new 1.5 ml tube and placed on ice. 30 µl of chromatin solution was used for each ChIP assay (~50K nuclei).  Preparation of immunoprecipitation beads: 5 µl of protein A Dynabeads (10001D, Invitrogen) were used in each MOWChIP assay. The beads were washed twice with IP buffer (20 mM tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100) and resuspended in 150 µl of IP buffer. The following antibodies were used in this work: anti-H3K27ac (ab4729, Abcam), 0.125 µg/assay; anti-H3K4me1 (39297, Active Motif), 0.5 µl/assay; anti-H3K4me3 (ab8580, Abcam), 0.125 µg/assay; anti-H3K27me3 (39155, Active Motif), 0.5 µg/assay; anti-H3K9me3 (ab8898, Abcam), 0.125 µg/assay. The suspension was incubated on a rotator at 4°C overnight. The beads were washed with IP buffer twice and resuspended in 5 µl of IP buffer for loading in the MOWChIP device.  MOWChIP: The microfluidics based MOWChIP process, including device fabrication and operation, was performed following our published protocol (Zhu, B., Hsieh, YP., Murphy, T.W. et al. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 14, 3366–3394 (2019).).  RNA extraction: Tissue slices were placed in 200 µl of RNAlater-ICE frozen tissue transition solution (AM7030, Thermo Fisher Scientific) prechilled to -80°C. They were then incubated at -20°C overnight. Each RNA-seq library was prepared from 10ng RNA extracted from the tissue. Two technical replicates were prepared for each sample. Total RNA was extracted from the incubated tissue using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen).
ChIP-seq: Libraries were prepared using 2S Plus DNA library kit (IDT) following the manufacturer’s protocol. 1 × EvaGreen dye (Biotium) was added to the qPCR amplification mixture to monitor progress of amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library size distribution was examined using TapeStation (Agilent) and concentration was quantified with Kapa Library Quantification kit (Kapa Biosystems).  RNA-seq: Extracted total RNA was resuspended in 4.5 μL of RNase-free water with 5% RNase inhibitor (40 U/μL) added. 2 μL of oligo-dT primer (10 μM), 2 μL of dNTP mix (10 mM) and 4.3 μL of total RNA solution were mixed, incubated at 72°C for 3 minutes and immediately put on ice. Then 1 μL of SuperScript II reverse transcriptase (200 U/μL), 0.5μL of RNase inhibitor (40 U/μl), 4μL of Superscript II first-strand buffer, 1 μL of DTT (100 mM), 4 μL of 5 M Betaine, 0.12 μL of 1 M MgCl2, 0.2 μL of TSO (100 μM), 0.88 μL of nuclease-free water were added to the 8.3 μl mixture mentioned above. The reverse transcription (RT) reaction mix was then incubated at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, and lastly 70°C for 15 minutes. The RT reaction mix was mixed with 25 μL KAPA HiFi HotStart ReadyMix, 0.5 μL IS PCR primers (10 μM), 2.5 μL Evagreen dye, and 2 μL nuclease-free water, and amplified with: 98°C for 1 minute, 9–11 cycles of 98°C 15 seconds, 67°C 30 seconds, 72°C 6 minutes. The cDNA was purified using 30 μL of SPRIselect beads and eluted in 5 μL of low EDTA TE buffer. The RNA-seq library was made using tagmentation. 3 μL of home-made Tn5 was mixed with 3 μL of 50 μM pre-annealed P5/P7 transposon and incubated at 37°C for 1 hour. Assembled P5 and P7 transposons were then mixed well to form Tn5 mix. 1 μL cDNA (600 pg) and 1 μL of tagmentation buffer (TNP92110, Lucigen) were added to 8 μL Tn5 mix, and the mixture was incubated at 37°C for 1 hour. 1 μL of 10X stop buffer (TNP92110, Lucigen) was then added to the mixture to quench tagmentation. 11 μL SPRIselect beads were used to purify tagmented cDNA. The cDNA was then eluted in 9.5 μL of low EDTA TE buffer. 25 μL of KAPA HiFi HotStart ReadyMix was incubated at 98°C for 30 seconds, mixed with 9.5 μL tagmented cDNA and incubated at 72°C for 5 minutes. 1.5 μL of 100 μM P5 primer, 1.5 μL of 100 μM P7 primer, 10 μL nuclease-free water and 2.5 μL Evagreen were then added and amplified with: 98°C for 30 seconds; 10-12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 30 seconds. Amplified cDNA libraries were purified with 50 μL SPRIselect beads and eluted in 8 μL of low EDTA TE buffer. The RNA library preparation is adapted from Smart-Seq2 workflow (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014).)

value: Lung

tag: disease state

value: Non-neoplastic


title: RB3823

type: genomic

description:
retinoblastoma cell line, parental
ryl_et_al_beta_matrix_cell_line.txt

hyb_protocol: Bisulfite treatment, whole-genome DNA amplification, hybridization and single-base extension, fluorescence staining and scanning of the chips were performed following the manufacturer´s instructions (Illumina).

scan_protocol: Standard Illumina Protocol

data_processing:
IDAT files generated on 450k and EPIC arrays were reduced to the 450K common probes and processed using minfi (version 1.36).  minfi's funnorm function was used for normalisation.  Batch correction was conducted for each array type using comBat (from sva version 3.42).
matrix processed value definition:  Normalized (minfi funnorm) Average Beta

label: Cy5 and Cy3

source_name: retinoblastoma cell line

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from fresh-frozen tumor samples and retinoblastoma cell lines was isolated as previously described (Lohmann et al., 1997, Schwermer et al., 2019)

value: retinoblastoma cell line

value: retinoblastoma

tag: growth protocol

value: Cell lines were cultivated in Dulbecco’s Modified Eagle Medium (ThermoFisher Scientific) supplemented with 15% fetal calf serum (Thermo Fisher Scientific), 11μM β-mercaptoethanol (MilliporeSigma) and 100U/ml penicillin/streptomycin (Thermo Fisher Scientific) in a humidified atmosphere with 5% CO2 at 37°C


title: RB355


title: RB383


title: Y79


title: ChIP-seq for MLLT3 in CB-HSPC-MLLT3-L-OE

value: MLLT3-L OE


title: RB522


title: ChIP-seq for MLLT3 in CB-HSPC-CTR


title: RB247C3


title: RB1021


title: RB_INF_1673

description:
relapse retinoblastoma tumor
ryl_et_al_beta_matrix_tumors.txt

source_name: retinoblastoma tumor, relapse

value: B


title: RB_INF_1024

value: A


title: 25-8-RNA-R1


title: 25-9-RNA-R1


title: RB_9

description:
primary retinoblastoma tumor
ryl_et_al_beta_matrix_tumors.txt

source_name: retinoblastoma tumor, primary


title: 25-7-RNA-R2


title: 25-8-RNA-R2


title: 25-7-RNA-R1


title: RB_7


title: cut80, K562 cells

value: marrow

value: marrow cancer cells

value: WT


title: RBL30


title: WERI-RB1


title: 25-6-RNA-R1

value: Tumor


title: 25-6-RNA-R2


title: 25-5-RNA-R2


title: RB_60


title: RB_61


title: 25-4-RNA-R2


title: RB_59


title: RB_6


title: RB_58


title: 25-5-RNA-R1


title: 25-4-RNA-R1


title: RB_56


title: 25-34-RNA-R1


title: 25-33-RNA-R2


title: RB_57


title: 25-33-RNA-R1


title: RB_55

value: C


title: RB_53


title: RB_54


title: RB_50


title: 25-31-RNA-R2


title: RB_5


title: 25-31-RNA-R1


title: 25-30-RNA-R2


title: RB_40


title: RB_4


title: 25-30-RNA-R1


title: RB_38


title: 25-29-RNA-R1


title: 25-34-RNA-R2


title: RB_37


title: RB_39


title: 25-28-RNA-R2


title: 25-28-RNA-R1


title: RB_34


title: 25-27N-RNA-R2


title: RB_32


title: RB_8


title: 25-27N-RNA-R1


title: RB_36


title: 25-26N-RNA-R2


title: 25-32-RNA-R2


title: 25-26N-RNA-R1


title: RB_30


title: 25-25N-RNA-R2


title: RB_3


title: RB_29


title: RB_27


title: 25-24N-RNA-R2


title: 25-29-RNA-R2


title: 25-24N-RNA-R1


title: RB_25


title: 25-23N-RNA-R2


title: RB_19


title: 25-32-RNA-R1


title: 25-22N-RNA-R2


title: RB_31


title: RB_17


title: 25-23N-RNA-R1


title: RB_16


title: RB_18


title: 25-21N-RNA-R2


title: 25-21N-RNA-R1


title: 25-22N-RNA-R1


title: RB_12


title: RB_15


title: 25-25N-RNA-R1


title: RB_14


title: RB_13


title: 25-20T-RNA-R2


title: 25-20T-RNA-R1


title: RB_11


title: 25-20N-RNA-R2


title: LDA_C22_iPSC

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description: methylation profiling using bisulfite converted

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing: Genome-wide methylation analysis was performed by the Illumina Infinium methylation Epic array on bisulfite converted DNA extracted from the three tissues of the patient. Data were analyzed using R version 4.1.0. Beta values (Bvalues) were derived from “idat” files by the “champ.load” module of the “ChAMP” R package (v.2.22.0), with quality control options set as default and array type as “EPIC.” To adjust the Bvalues of type 2 probes, we applied BMIQ normalization with the default options for array type as “EPIC.”

label_protocol: Standard llumina Protocol

growth_protocol: iPSC were grown in StemMACS™ iPS-Brew XF (Miltenyi Biotec) at 37°C and 5% CO2

extract_protocol: Genomic DNA was extracted from iPSCs (passages X) and parental blood using the Wizard ® Genomic DNA kit (Promega)

tag: gender

value: F

tag: condition

value: Control

value: iPSC


title: RB_10


title: 25-20N-RNA-R1


title: 25-19T-RNA-R2


title: LDA_C14_iPSC


title: pYM_B9_iPSC

value: M

value: ICF syndrome type 2 (ICF2)


title: 25-19N-RNA-R1

value: Lung

value: Non-neoplastic


title: 25-19T-RNA-R1


title: pYM_C6_iPSC


title: 25-18T-RNA-R1


title: 25-18T-RNA-R2


title: pYM_ICF2_Blood

value: Blood


title: 25-18N-RNA-R2


title: 25-19N-RNA-R2


title: 25-18N-RNA-R1


title: 25-17T-RNA-R1


title: 25-17N-RNA-R1


title: 25-17N-RNA-R2


title: 25-17T-RNA-R2


title: 25-16T-RNA-R2


title: 25-15T-RNA-R2


title: 25-16N-RNA-R2


title: 25-15T-RNA-R1


title: 25-16N-RNA-R1


title: 25-14T-RNA-R2


title: 25-15N-RNA-R1


title: 25-16T-RNA-R1


title: 25-14T-RNA-R1


title: 25-15N-RNA-R2


title: 25-14N-RNA-R2


title: 25-14N-RNA-R1


title: 25-13T-RNA-R2


title: 25-13N-RNA-R2


title: 25-13T-RNA-R1


title: 25-13N-RNA-R1


title: 25-12-RNA-R2


title: 25-12-RNA-R1


title: 25-10-RNA-R2


title: 25-10-RNA-R1


title: 25-9-H3K9me3-R2


title: 25-9-H3K9me3-R1


title: genomic DNA from VACO400

city: Candiolo

first: Federica

last: Di Nicolantonio

state: Torino

address: Candiolo Cancer Institute FPO-IRCCS, SP142, km 3.95

department: Department of Oncology

institute: University of Torino

description: Parental CRC cell line grown in vitro without any treatment

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip microarray using standard Illumina Infinium HD methylation protocol

scan_protocol: Arrays were imaged using iScan with the standard recommended Illumina scanner setting

data_processing: EPIC raw data (IDAT files) were processed using the minfi R Bioconductor package and corresponding annotation packages. In each sample, probes with detection p-value > 0.05 were masked in the RGChannelSet. In addition, cross-reactivity probes and probes matching SNPs at the target CpG site were filtered using previously published lists. Then, methylation and unmethylation signals were obtained for each CpG site using the preprocessNoob function and beta-values were computed. Results obtained in all samples were subsequently merged in a single beta-matrix and CpG sites that are located on sex chromosomes or chrM were excluded.

source_name: CRC cell line

label_protocol: Standard Illumina labelling protocol

growth_protocol: All cells were maintained in the media recommanded by supplier

extract_protocol: Genomic DNA was extracted Maxwell RSC Blood DNA kit (Promega)

treatment_protocol: All cells were maintained in absence of drug

value: CRC cell line


title: genomic DNA from LIM1863


title: genomic DNA from KP363T


title: 25-8-H3K9me3-R2


title: genomic DNA from JVE528


title: genomic DNA from KP7038T


title: genomic DNA from V9P


title: genomic DNA from JVE253


title: genomic DNA from JVE059


title: genomic DNA from LM0701_A_XL


title: 25-7-H3K9me3-R1


title: genomic DNA from JVE241


title: genomic DNA from JVE127


title: genomic DNA from JVE187


title: 25-6-H3K9me3-R2


title: 25-8-H3K9me3-R1


title: genomic DNA from ISRECO1


title: genomic DNA from JVE015


title: genomic DNA from IRCC5_A_XL


title: genomic DNA from JVE367


title: genomic DNA from JVE207


title: genomic DNA from JVE044


title: genomic DNA from JVE109


title: genomic DNA from KP283T


title: 25-5-H3K9me3-R1


title: genomic DNA from LM0201_A_XL


title: genomic DNA from IRCC72_A_XL


title: 25-4-H3K9me3-R2


title: genomic DNA from JVE103


title: genomic DNA from JVE192


title: genomic DNA from JVE371


title: 25-33-H3K9me3-R2


title: genomic DNA from IRCC3_HL


title: 25-5-H3K9me3-R2


title: 25-4-H3K9me3-R1


title: 25-7-H3K9me3-R2


title: 25-32-H3K9me3-R1


title: genomic DNA from RW2982


title: 25-6-H3K9me3-R1


title: genomic DNA from IRCC3_XL


title: 25-34-H3K9me3-R1


title: 25-33-H3K9me3-R1


title: genomic DNA from IRCC22_XL


title: 25-31-H3K9me3-R1


title: 25-32-H3K9me3-R2


title: 25-30-H3K9me3-R1


title: 25-29-H3K9me3-R2


title: 25-34-H3K9me3-R2


title: 25-31-H3K9me3-R2


title: 25-28-H3K9me3-R2


title: 25-29-H3K9me3-R1


title: genomic DNA from IRCC1_XL


title: 25-27N-H3K9me3-R2


title: 25-30-H3K9me3-R2


title: 25-27N-H3K9me3-R1


title: genomic DNA from IRCC10_A_HL


title: 25-28-H3K9me3-R1


title: 25-26N-H3K9me3-R1


title: 25-26N-H3K9me3-R2


title: genomic DNA from HROC57


title: 25-25N-H3K9me3-R2


title: 25-25N-H3K9me3-R1


title: genomic DNA from HROC60


title: 25-24N-H3K9me3-R2


title: genomic DNA from HROC383_T0M2


title: genomic DNA from JVE114


title: genomic DNA from HROC43


title: 25-23N-H3K9me3-R2


title: genomic DNA from HROC50_T1M5


title: 25-24N-H3K9me3-R1


title: genomic DNA from HROC324


title: 25-23N-H3K9me3-R1


title: genomic DNA from HROC59


title: genomic DNA from HROC313_MET1


title: genomic DNA from HROC348


title: 25-22N-H3K9me3-R1


title: genomic DNA from HROC370


title: 25-21N-H3K9me3-R2


title: genomic DNA from HROC348_MET


title: genomic DNA from HROC40


title: genomic DNA from HROC383


title: 25-21N-H3K9me3-R1


title: genomic DNA from HROC374


title: genomic DNA from HROC334


title: genomic DNA from HROC277_MET2


title: 25-20T-H3K9me3-R2


title: 25-22N-H3K9me3-R2


title: genomic DNA from HROC32_T3M1


title: genomic DNA from HROC284_MET


title: genomic DNA from HROC277_T0M1


title: 25-20T-H3K9me3-R1


title: 25-19T-H3K9me3-R2


title: 25-20N-H3K9me3-R1


title: 25-19N-H3K9me3-R2


title: genomic DNA from HROC278_T0M1


title: genomic DNA from HROC239_T0M1


title: 25-19N-H3K9me3-R1


title: genomic DNA from HROC222_T1M2


title: 25-19T-H3K9me3-R1


title: 25-18T-H3K9me3-R2


title: 25-18T-H3K9me3-R1


title: genomic DNA from HROC278_MET


title: genomic DNA from HROC300_T2M1


title: genomic DNA from HROC257_T0M1


title: 25-18N-H3K9me3-R2


title: genomic DNA from HROC309


title: 25-18N-H3K9me3-R1


title: 25-17T-H3K9me3-R2


title: 25-20N-H3K9me3-R2


title: 25-17T-H3K9me3-R1


title: 25-17N-H3K9me3-R2


title: 25-17N-H3K9me3-R1


title: genomic DNA from HROC173


title: genomic DNA from HROC147_T0M1


title: 25-16T-H3K9me3-R2


title: genomic DNA from HROC212


title: genomic DNA from HROC183


title: 25-16T-H3K9me3-R1


title: genomic DNA from HROC113


title: 25-16N-H3K9me3-R2


title: 25-15T-H3K9me3-R2


title: genomic DNA from HROC131_T0M3


title: 25-16N-H3K9me3-R1


title: 25-15T-H3K9me3-R1


title: 25-15N-H3K9me3-R2


title: 25-15N-H3K9me3-R1


title: 25-14T-H3K9me3-R2


title: 25-14T-H3K9me3-R1


title: genomic DNA from HROC112_MET


title: 25-14N-H3K9me3-R2


title: genomic DNA from CRC0080_XL


title: genomic DNA from CRC0313_XL


title: 25-14N-H3K9me3-R1


title: 25-13T-H3K9me3-R2


title: genomic DNA from CRC1360_XL


title: genomic DNA from CRC0781_XL


title: genomic DNA from CRC0438_XL


title: genomic DNA from HROC147_MET


title: genomic DNA from COGA10


title: 25-13T-H3K9me3-R1


title: genomic DNA from CRC0778_XL


title: genomic DNA from B1003_XL5


title: genomic DNA from CRC0104_XL


title: genomic DNA from CRC0691_XL


title: genomic DNA from CRC0394_XL


title: 25-13N-H3K9me3-R2


title: genomic DNA from CRC0322_XL


title: genomic DNA from CR4


title: 25-13N-H3K9me3-R1


title: 25-12-H3K9me3-R2


title: genomic DNA from HHC6548


title: 25-12-H3K9me3-R1


title: 25-10-H3K9me3-R2


title: genomic DNA from CRC0558_XL


title: genomic DNA from HROBMCO1


title: 25-9-H3K4me1-R2

value: H3K4me1 (Active Motif, #39297)


title: genomic DNA from CRC0078_XL


title: 25-9-H3K4me1-R1


title: genomic DNA from CRC0174_XL


title: genomic DNA from CRC0740_XL


title: 25-8-H3K4me1-R2


title: 25-10-H3K9me3-R1


title: high-grade serous ovarian cancer_after chemotherapy_29

city: Chuo-ku

first: Takahiro

last: Ebata

state: Tokyo

address: 5-1-1, Tsukiji

country: Japan

institute: National Cancer Center Research Institute

description:
high-grade serous ovarian cancer after chemotherapy
OV_No46

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

extract_protocol: Genomic DNA was extracted using the standard phenol/chloroform method.

value: Female

value: high-grade serous ovarian cancer


title: 25-8-H3K4me1-R1


title: 25-7-H3K4me1-R2


title: genomic DNA from HROC107_cT0M2


title: 25-7-H3K4me1-R1


title: genomic DNA from HROC126


title: 25-6-H3K4me1-R2


title: 25-6-H3K4me1-R1


title: genomic DNA from B1003_XLSP


title: 25-5-H3K4me1-R2


title: high-grade serous ovarian cancer_after chemotherapy_28

description:
high-grade serous ovarian cancer after chemotherapy
OV_No44


title: 25-4-H3K4me1-R2


title: high-grade serous ovarian cancer_after chemotherapy_30

description:
high-grade serous ovarian cancer after chemotherapy
OV_No47


title: 25-4-H3K4me1-R1


title: high-grade serous ovarian cancer_after chemotherapy_27

description:
high-grade serous ovarian cancer after chemotherapy
OV_No43


title: 25-34-H3K4me1-R2


title: 25-34-H3K4me1-R1


title: Visium Mouse 5 Mixture (Cerebellum + adjacent region)

city: Boston

first: Luli

last: Zou

address: 677 Huntington Ave

institute: Harvard

data_processing:
Slide-seq libraries were processed with the slideseq-tools pipeline (https://github.com/MacoskoLab/slideseq-tools) and then re-aligned to a custom transcriptome. For longer read libraries (Mouse 3 Slide-seq), we used Atropos to trim adapter sequences and low quality bases. 10x Genomics Visium was performed on two mice (Mice 4,5) on 10umn-thick coronal slices of the cerebellum. Visium libraries were processed with the 10x Genomics Space Ranger 1.1.0 pipeline and then re-aligned to a custom transcriptome. We generated a pooled CASTx129 transcriptome using the command create-hybrid from the EMASE software on the CAST and 129 transcript fasta files downloaded from ftp://churchill-lab.jax.org/software/g2gtools/mouse/R84-REL1505/. We then aligned reads to this pooled transcriptome with bowtie2 using the parameters -k 100 -p 16 --very-sensitive. This method of alignment ensures there is no reference bias. The multi-mapping parameter k=100 was chosen to report a large amount of multi-maps as bowtie2 randomly reports multi-mapping locations (in order of increasing number of mismatches). We used a custom script (https://github.com/lulizou/spASE/blob/master/scripts/processBowtie2.py) for processing the aligned BAM file to create a gene UMI count matrix only from reads that uniquely aligned to one gene and one allele. We conservatively restricted attention to alignments with 3 or fewer mismatches and only considered alignments that had the fewest number of mismatches for that read. We merged the reads from samples that had two serial sections: Mouse 1 hippocampus, Mouse 3 hippocampus, and Mouse 3 cerebellum.
Assembly: mm10
Supplementary files format and content: rds files containing the RCTD objects for each sample

source_name: brain

extract_protocol:
We used female CAST/EiJ x 129S1/SvImJ mice obtained from Jackson Laboratories. We obtained fresh frozen blocks and used 10um-thick coronal slices of the hippocampus or cerebellum.
Slide-seqV2 (Stickels et al. 2022) or Visium (10X Genomics) was performed as described previously
spatial transcriptomics

value: brain


title: 25-33-H3K4me1-R1


title: 25-33-H3K4me1-R2


title: 25-5-H3K4me1-R1


title: Visium Mouse 4 Cerebellum


title: 25-32-H3K4me1-R2


title: high-grade serous ovarian cancer_after chemotherapy_26

description:
high-grade serous ovarian cancer after chemotherapy
OV_No41


title: library4_Src_aPCA_wt

city: Barcelona

first: cristina

last: Hidalgo-Carcedo

address: Dr. Aiguader 88

country: Spain

institute: CRG

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: does not apply
Supplementary files format and content: MS Excel format; contains Dimsum fitness estimates, inferred growth rates and their corresponding errors for all libraries; see README tab for a description of all columns

growth_protocol: For each library and assay (abundancePCA and bindingPCA) each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, saturated cells were diluted again to OD600nm = 0.1 in SC -URA/MET/ADE media and allowed to grow 4 generations until OD600nm = 1.6 at 30ºC and 200rpm. A fraction of the culture was then used to inoculate 200mL of competition media containing methotrexate at a starting OD600nm = 0.05, and the rest was harvested and pellets frozen and stored as INPUT.  Cells in competition media were allowed to grow for 3-5 generations, collected and frozen and stored as OUTPUT.

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer, frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC at least for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (50 µL of QIAEX II beads, QIAGEN). The samples were washed twice with PE buffer and eluted twice by 125 µL of 10 mM Tris-HCI buffer, pH 8.5. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
The sequencing libraries were constructed in two consecutive PCR reactions. The first PCR (PCR1) was designed to amplify the mutated protein of interest and to increase the nucleotide complexity of the first sequenced bases by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) was necessary to add the remainder of the Illumina adapter and demultiplexing indexes. PCR2 reactions were run for each sample independently using Hot Start High-Fidelity DNA Polymerase. In this second PCR the remaining parts of the Illumina adapters were added to the library amplicon. The forward primer (5’ P5 Illumina adapter) was the same for all samples in libraries 1-3 and containing a different barcode index in library 4. The reverse primer (3’ P7 Illumina adapter) differed by the barcode index  to be subsequently pooled together and demultiplex them after deep sequencing. All samples were pooled in an equimolar ratio and gel purified using the QIAEX II Gel Extraction Kit. The purified amplicon library pools were subjected to Illumina 150bp paired-end Nextseq500 (libraries 1-3) or Nextseq2000 (library 4) sequencing at the CRG Genomics Core Facility.
DNA-seq of PCR amplicons


title: Slide-seq Mouse 3 Cerebellum Puck 2


title: 25-32-H3K4me1-R1


title: 25-31-H3K4me1-R2


title: 25-31-H3K4me1-R1


title: library4_Src_aPCA_output_bio_rep_3


title: high-grade serous ovarian cancer_after chemotherapy_25

description:
high-grade serous ovarian cancer after chemotherapy
OV_No39


title: Slide-seq Mouse 3 Cerebellum Puck 1


title: high-grade serous ovarian cancer_after chemotherapy_21

description:
high-grade serous ovarian cancer after chemotherapy
OV_No34


title: library4_Src_aPCA_output_bio_rep_2


title: high-grade serous ovarian cancer_after chemotherapy_23

description:
high-grade serous ovarian cancer after chemotherapy
OV_No36


title: 25-30-H3K4me1-R1


title: Slide-seq Mouse 3 Hippocampus Puck 2


title: 25-30-H3K4me1-R2


title: 25-29-H3K4me1-R2


title: high-grade serous ovarian cancer_after chemotherapy_19

description:
high-grade serous ovarian cancer after chemotherapy
OV_No29


title: library4_Src_aPCA_output_bio_rep_1


title: high-grade serous ovarian cancer_after chemotherapy_24

description:
high-grade serous ovarian cancer after chemotherapy
OV_No37


title: 25-29-H3K4me1-R1


title: high-grade serous ovarian cancer_after chemotherapy_20

description:
high-grade serous ovarian cancer after chemotherapy
OV_No32


title: 25-28-H3K4me1-R2


title: library4_Src_aPCA_input_bio_rep_3


title: 25-28-H3K4me1-R1


title: Slide-seq Mouse 2 Hippocampus Puck 2


title: Slide-seq Mouse 3 Hippocampus Puck 1


title: high-grade serous ovarian cancer_after chemotherapy_18

description:
high-grade serous ovarian cancer after chemotherapy
OV_No28


title: library4_Src_aPCA_input_bio_rep_2


title: high-grade serous ovarian cancer_after chemotherapy_13

description:
high-grade serous ovarian cancer after chemotherapy
OV_No22


title: 25-27N-H3K4me1-R1


title: 25-27N-H3K4me1-R2


title: Slide-seq Mouse 2 Hippocampus Puck 1


title: library4_Src_aPCA_input_bio_rep_1


title: 25-26N-H3K4me1-R1


title: 25-25N-H3K4me1-R2


title: Slide-seq Mouse 1 Hippocampus Puck 2


title: 25-25N-H3K4me1-R1


title: high-grade serous ovarian cancer_after chemotherapy_15

description:
high-grade serous ovarian cancer after chemotherapy
OV_No24


title: 25-24N-H3K4me1-R2


title: Slide-seq Mouse 1 Hippocampus Puck 1


title: high-grade serous ovarian cancer_after chemotherapy_09

description:
high-grade serous ovarian cancer after chemotherapy
OV_No14


title: delta-zntR strain_rep3

city: Yangzhou

first: Chengkun

last: Zheng

address: No.48 East Wenhui Road

institute: Yangzhou university

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Assembly: Vibrio parahaemolyticus RIMD2210633, complete genome (NC_004603.1; NC_004605.1)
Supplementary files format and content: gene expression (read counts and fpkm for each stra).

organism: Vibrio parahaemolyticus

source_name: delta-zntR on RIMD 2210633 background

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: delta-zntR on RIMD 2210633 background

tag: phase

value: mid-exponential phase


title: delta-zntR strain_rep1


title: TWT3

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm39/mm39) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Assembly: GRCm39/mm39
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: Cpt1abDKOvsControl_deg.txt includes the differential analysis results of all genes when comparing Cpt1a;Cpt1b liver-specific DKO to Cpt1a;1b;2 triple floxed control. Tab-delimited text file.
Supplementary files format and content: Cpt1ab2TKOvsCpt2KO_deg.txt includes the differential analysis results of all genes when comparing Cpt1a;1b;2 liver-specific TKO to Cpt2 liver-specific KO. Tab-delimited text file.
Supplementary files format and content: Cpt1abDKOvsCpt1ab2TKO_deg.txt includes the differential analysis results of all genes when comparing Cpt1a;1b liver-specific DKO to Cpt1a;1b;2 liver-specific TKO. Tab-delimited
Supplementary files format and content: Cpt1ab2TKOvsCpt2PparaDKO_deg.txt includes the differential analysis results of all genes when comparing Cpt1a;1b;2 liver-specific TKO to PPARA;Cpt2 liver-specific DKO. Tab-delimited text file.
Supplementary files format and content: Cpt1abDKOvsCpt2KO_deg.txt includes the differential analysis results of all genes when comparing Cpt1a;1b liver-specific DKO to Cpt2 liver-specific KO . Tab-delimited text file.
Supplementary files format and content: Cpt1abDKOvsCpt2PparaDKO_deg.txt  includes the differential analysis results of all genes when comparing Cpt1a;1b liver-specific DKO to PPARA;Cpt2 liver-specific DKO. Tab-delimited
Supplementary files format and content: Cpt1ab2TKOvsControl_deg.txt includes the differential analysis results of all genes when comparing Cpt1a;1b;2 liver-specific TKO to Cpt1a;1b;2 triple floxed control. Tab-delimited text file.
Supplementary files format and content: Cpt2KOvsControl_deg.txt includes the differential analysis results of all genes when comparing Cpt2 liver-specific KO to Cpt1a;1b;2 triple floxed control . Tab-delimited text file.
Supplementary files format and content: Cpt2PparaDKOvsControl_deg.txt  includes the differential analysis results of all genes when comparing PPARA;Cpt2 liver-specific DKO to Cpt1a;1b;2 triple floxed control. Tab-delimited
Supplementary files format and content: Cpt2PparaDKOvsCpt2KO_deg.txt includes the differential analysis results of all genes when comparing PPARA;Cpt2 liver-specific DKO to Cpt2 liver-specific KO. Tab-delimited

source_name: liver

extract_protocol:
Total RNA was extracted from flash frozen liver tissue using TRIzol reagent (Invitrogen for Thermo Fisher Scientific, 15596026) with additional purification using RNeasy Mini Kit (Qiagen, 74106), as per manufacturers’ instructions. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc (https://en.novogene.com/services/research-services/transcriptome-sequencing/).
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

value: liver

value: CPT1A/1B/2 triple floxed control

value: 24hr fast


title: TWT4


title: delta-zntR strain_rep2


title: high-grade serous ovarian cancer_after chemotherapy_07

description:
high-grade serous ovarian cancer after chemotherapy
OV_No12


title: high-grade serous ovarian cancer_after chemotherapy_12

description:
high-grade serous ovarian cancer after chemotherapy
OV_No19


title: 25-23N-H3K4me1-R1


title: TWT2


title: 25-21N-H3K4me1-R2


title: high-grade serous ovarian cancer_after chemotherapy_05

description:
high-grade serous ovarian cancer after chemotherapy
OV_No9


title: The wild type strain_rep2


title: 25-20T-H3K4me1-R1

value: Tumor


title: 25-20T-H3K4me1-R2


title: TWT1


title: The wild type strain_rep1


title: high-grade serous ovarian cancer_after chemotherapy_03

description:
high-grade serous ovarian cancer after chemotherapy
OV_No4


title: high-grade serous ovarian cancer_after chemotherapy_02

description:
high-grade serous ovarian cancer after chemotherapy
OV_No2


title: high-grade serous ovarian cancer_after chemotherapy_14

description:
high-grade serous ovarian cancer after chemotherapy
OV_No23


title: 25-22N-H3K4me1-R1


title: high-grade serous ovarian cancer_after chemotherapy_04

description:
high-grade serous ovarian cancer after chemotherapy
OV_No7


title: high-grade serous ovarian cancer_after chemotherapy_06

description:
high-grade serous ovarian cancer after chemotherapy
OV_No11


title: 25-20N-H3K4me1-R2


title: Y79

description:
retinoblastoma cell line, parental
ryl_et_al_rb_cell_lines_log1ptpm.txt

tag: cell type

value: retinoblastoma

value: WT


title: 25-20N-H3K4me1-R1

tag: tissue


title: TKO4

value: CPT1A/1B/2 liver-specific triple KO


title: 25-19T-H3K4me1-R2

value: Lung


title: 25-26N-H3K4me1-R2

value: Non-neoplastic


title: high-grade serous ovarian cancer_after chemotherapy_10

description:
high-grade serous ovarian cancer after chemotherapy
OV_No16


title: WERI-RB1


title: 25-19T-H3K4me1-R1


title: 25-19N-H3K4me1-R2


title: TKO2


title: RB522


title: high-grade serous ovarian cancer_after chemotherapy_01

description:
high-grade serous ovarian cancer after chemotherapy
OV_No1


title: high-grade serous ovarian cancer_after chemotherapy_16

description:
high-grade serous ovarian cancer after chemotherapy
OV_No25


title: TKO1


title: 25-18T-H3K4me1-R2


title: high-grade serous ovarian cancer_after chemotherapy_11

description:
high-grade serous ovarian cancer after chemotherapy
OV_No18


title: TKO3


title: 25-22N-H3K4me1-R2


title: RB383


title: 25-18T-H3K4me1-R1


title: 25-18N-H3K4me1-R2


title: PPARDKO4

value: PPAR;CPT2 liver-specific double KO


title: 25-24N-H3K4me1-R1


title: RB3823


title: 25-19N-H3K4me1-R1


title: 25-18N-H3K4me1-R1


title: RB355


title: 25-17T-H3K4me1-R1


title: PPARDKO3


title: PPARDKO2


title: RB247C3


title: 25-17N-H3K4me1-R2


title: 25-16T-H3K4me1-R2


title: 25-17N-H3K4me1-R1


title: PPARDKO1


title: RB1021


title: 25-16N-H3K4me1-R2


title: CPT24

value: CPT2 liver-specific KO


title: The wild type strain_rep3

tag: strain


title: 25-16N-H3K4me1-R1

value: H3K4me1 (Active Motif, #39297)


title: CPT23


title: 25-17T-H3K4me1-R2


title: 25-15T-H3K4me1-R2


title: 25-15N-H3K4me1-R2


title: RB_58

description:
primary retinoblastoma tumor
ryl_et_al_rb_tumors_log1ptpm.txt

tag: cluster ryl_et_al

value: B


title: 25-15T-H3K4me1-R1

tag: chip antibody


title: RB_57


title: 25-15N-H3K4me1-R1


title: CPT22

tag: genotype


title: 25-21N-H3K4me1-R1


title: 25-14T-H3K4me1-R1


title: RB_56


title: CPT21


title: 25-14T-H3K4me1-R2


title: 25-14N-H3K4me1-R2


title: RB_61

value: A


title: AB4

value: CPT1A;CPT1B liver-specific double KO


title: 25-14N-H3K4me1-R1


title: high-grade serous ovarian cancer_after chemotherapy_17

description:
high-grade serous ovarian cancer after chemotherapy
OV_No27

value: Female

tag: age

value: high-grade serous ovarian cancer


title: 25-13T-H3K4me1-R2


title: AB3

value: liver

tag: treatment


title: RB_54

tag: rb1 status


title: 25-13T-H3K4me1-R1


title: 25-23N-H3K4me1-R2


title: 25-13N-H3K4me1-R2


title: AB2


title: RB_53

tag: mycn amplification


title: 25-13N-H3K4me1-R1


title: 25-12-H3K4me1-R2


title: AB1


title: RB_55

value: C


title: RB_52


title: CPT1A4

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm38/mm10) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: Cpt2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Cpt2 liver-specific KO to Rab30;Cpt2 floxed control. Tab-delimited text file.
Supplementary files format and content: Cpt1a_AlbCrevsRab30Cpt2_f_deg_all.txt includes the differential analysis results of all genes when comparing Cpt1a liver-specific KO to Rab30;Cpt2 floxed control . Tab-delimited text file.
Supplementary files format and content: Cpt1a_AlbCrevsCpt2_AlbCre_deg.txt  includes the differential analysis results of all genes when comparing Cpt1a liver-specific KO toCpt2 liver-specific KO. Tab-delimited

value: Cpt1a liver-specific KO

value: 24hr fast


title: high-grade serous ovarian cancer_after chemotherapy_08

description:
high-grade serous ovarian cancer after chemotherapy
OV_No13


title: RB_51

value: retinoblastoma


title: CPT1A3


title: 25-9-H3K4me3-R2


title: RB_50


title: 25-9-H3K4me3-R1


title: RB_49


title: 25-8-H3K4me3-R1


title: CPT1A1


title: 25-10-H3K4me1-R1


title: 25-33-H3K4me3-R1

value: Tumor


title: RB_48


title: 25-33-H3K4me3-R2


title: 25-32-H3K4me3-R2


title: CPT1A2


title: 25-12-H3K4me1-R1


title: 25-32-H3K4me3-R1


title: 25-10-H3K4me1-R2


title: 25-8-H3K4me3-R2


title: 25-31-H3K4me3-R1


title: 25-30-H3K4me3-R2


title: Overexpression_western_diet_rep3

city: Boca Raton

first: Claudia

last: Rodrigues

state: Florida

address: 777 Glades Rd, BC-71, Rm. 224

department: Biomedical Science

institute: Florida Atlantic University

data_processing:
Raw data of fastq format were processed through in-house perl scripts. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Excel worksheet including raw counts for each sample
Supplementary files format and content: Excel worksheet including FPKM values for each sample

source_name: skeletal muscle

extract_protocol:
RNA was extracted from skeletal muscle harvested from control and transgenic mice using TRI-reagent (Molecular Resource Center), followed by in-column DNase-digestion using RNeasy kit (Qiagen). Samples were processed according to the manufacturer's instructions. RNA concentration was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific), and RNA integrity using an Agilent BioAnalyzer 2100 (Agilent Technologies).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: For diet-induced obesity experiments, mice were exposed to control (#TD.08485) or high-fat diet (#TD.88137) (Teklad, Indianapolis, IN, USA) for a total period of 20-weeks. Induction of c-Myc overexpression was performed between 4-6-weeks of age through withdrawal from the doxycycline diet (#TD.01306, Teklad, Indianapolis, IN, USA).

value: skeletal muscle

value: FVB/N

tag: Sex

value: Male

value: Endothelial c-Myc overexpression

value: Western Diet


title: Overexpression_western_diet_rep4


title: 25-31-H3K4me3-R2

value: Lung


title: RB_45

data_processing:
Assembly: hg38
Illumina bcl2fastq (2.20) was used to demultiplex the sequenced reads
For paired end sequencing, adapter trimming was performed with skewer (version 0.2.2) (Jiang et al. 2014)
For single read sequencing, adapter trimming was performed automatically with cutadapt
Sample specific fastq files were aligned to the reference transcriptome (GRCh38) by kallisto running 100 bootstraps
Differential gene expression analysis was performed with sleuth
Expression values were exported from the sleuth object as normalized TPM values
Supplementary files format and content: tab-delimited text file includes log2-transformed TPM+1 values for each sample from 52 retinoblastoma patients
Supplementary files format and content: tab-delimited text file includes log2-transformed TPM+1 values for each sample from 8 retinoblastoma cell lines
Supplementary files format and content: tab-delimited text file containing Arriba output
Supplementary files format and content: tab-delimited text file containing output of Wald test (sleuth) for significant differences between MYCNKD_doxy_positive vs MYCNKD_doxy_negative cells


title: 25-30-H3K4me3-R1


title: Overexpression_western_diet_rep2


title: 25-29-H3K4me3-R1


title: 25-29-H3K4me3-R2


title: Overexpression_western_diet_rep1


title: RB_47


title: 25-28-H3K4me3-R2


title: RB_44


title: 25-28-H3K4me3-R1


title: Adult healthy gingiva

city: London

first: Inês

last: Sequeira

address: Institute of Dentistry, 4 Newark street

country: United Kingdom

institute: Queen Mary University of London

description: 10x genomics

data_processing:
The cell ranger-6.0.1 pipeline was used for processing of the scRNAseq data files prior to analysis according to the instructions provided by 10x Genomics. Briefly, base call files obtained from each of the HiSeq2500 flow cells used were demultiplexed by calling the ‘cellranger mkfastq’. Resulting FASTQ files were aligned to the mouse reference genome(GRCm38/mm10) and subsequently filtered and had barcodes and unique molecular identifiers counted and count files generated for each sample. The raw count matrix output from CellRanger were then processed by the ambient RNA removal tool CellBender (Fleming et al., 2022), giving an output filtered count matrix file.
Assembly: GRCm38/mm10
Supplementary files format and content: h5ad format file with filtered count matrix

extract_protocol:
Freshly collected gingival tissues from 3 animals (2 males and 1 female) were processed together immediately after dissection. Tissue was transferred to a sterile petri dish with RPMI medium and chopped before transferring total volume to a 50 mL tube. Tissue was digested for 45 min at 37°C with intermittent shaking (170 rpm) using the enzymes from the Miltenyi Mouse-Tumor Dissociation kit (#130-096-730). The resulting cell suspension was consecutively filtered through a 100 µm and a 70 µm cell strainers to ensure a single-cell preparation and cells collected by centrifugation (1200 rpm for 5 min at 10°C).
Single-cell cDNA library was prepared using the 10X Genomics Chromium Single Cell 3’ kit (v3.1 Chemistry Dual Index). The prepared library was sequenced on Illumina® NovaSeq™6000 (2x150 bp) with a targeted sequencing depth of ~30,000 reads/cell.

value: Wild type

value: healthy

tag: developmental stage

value: Adult (P28)

value: pooled male and female


title: RB_46

extract_protocol:
Total RNA from primary tumor samples was isolated using the RNeasy Mini Kit (Qiagen) or Monarch Total RNA Miniprep kit (New England Biolabs GmbH) Total RNA from retinoblastoma cells was isolated using Rneasy mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer's protocols.

value: A


title: 25-27N-H3K4me3-R2

tag: disease state

value: Non-neoplastic


title: 25-27N-H3K4me3-R1


title: Overexpression_control_diet_rep3

value: Control Diet


title: Overexpression_control_diet_rep4


title: 25-26N-H3K4me3-R2


title: RB_42


title: high-grade serous ovarian cancer_after chemotherapy_22

description:
high-grade serous ovarian cancer after chemotherapy
OV_No35

value: Female

value: high-grade serous ovarian cancer


title: RB_41

value: retinoblastoma


title: 25-26N-H3K4me3-R1


title: Overexpression_control_diet_rep2


title: 25-25N-H3K4me3-R2


title: 25-24N-H3K4me3-R2


title: 25-25N-H3K4me3-R1


title: 25-24N-H3K4me3-R1


title: Overexpression_control_diet_rep1


title: RB_39


title: Control_western_diet_rep3

value: Control


title: RB_43


title: Control_western_diet_rep2

value: skeletal muscle


title: RB_38

value: B


title: 25-23N-H3K4me3-R1


title: 25-22N-H3K4me3-R1


title: 25-22N-H3K4me3-R2


title: RB_37

value: C


title: RB_36


title: 25-21N-H3K4me3-R2


title: 25-21N-H3K4me3-R1


title: Control_control_diet_rep3

value: FVB/N

value: Male


title: 25-20T-H3K4me3-R1

value: Lung

value: Tumor


title: Control_western_diet_rep1

value: Western Diet


title: Control_control_diet_rep2


title: RB_35


title: 25-20T-H3K4me3-R2


title: 25-20N-H3K4me3-R1


title: RB_40


title: Control_control_diet_rep1


title: 25-19T-H3K4me3-R2


title: 25-23N-H3K4me3-R2


title: RB_34


title: 25-19T-H3K4me3-R1


title: 25-19N-H3K4me3-R2


title: RB_32


title: RB_33


title: 25-19N-H3K4me3-R1


title: PM, IL4++ONX-0914, RNA-Seq, replicate3

city: Shenzhen

first: xing

last: shi

state: Guangdong

address: Luohu

department: Department of Respiratory and Critical Care Medicine

institute: Shenzhen Institute of Respiratory Disease

data_processing:
Raw sequence reads underwent quality evaluation using FastQC v0.11.9. Trimming of low-quality bases (<20) and removal of adapter sequences from raw reads was performed using Cutadapt v2.8 before alignment. Alignment to the mm10 reference genome was carried out using Bowtie2 v2.2.5 with the option “—very-sensitive”.To ensure data integrity, duplicate sequences were removed using MarkDuplicates v3.0.0 implemented in Picard tools (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: comma-separated values files include raw counts data for each sample

source_name: peritoneal macrophages

extract_protocol:
PMs from two to three mice in each group were pooled to obtain 50,000 cells for each replicate, and four independent replicates were analyzed for each group. Total RNA was extracted from each sample using the RNA isolater kit (Vazyme, R401-01, Nanjing, China).
Complementary DNA (cDNA) libraries were prepared using the HiScript II Q RT SuperMix kit (Vazyme, R223-01). After quality control assessment with Qubit and Agilent 5400 system (Agilent, USA), the qualified cDNA libraries were sequenced on Illumina platforms using PE150 sequencing.

value: peritoneal macrophages


title: PM, IL4++ONX-0914, RNA-Seq, replicate4


title: 25-18T-H3K4me3-R2


title: RB_31

city: Essen

first: Petra

address: Hufelandstraße 55

institute: University Hospital Essen

source_name: retinoblastoma


title: PM, IL4++ONX-0914, RNA-Seq, replicate2


title: 25-18T-H3K4me3-R1


title: 25-18N-H3K4me3-R2


title: PM, IL4++ONX-0914, RNA-Seq, replicate1


title: 25-20N-H3K4me3-R2


title: 25-17T-H3K4me3-R2


title: 25-18N-H3K4me3-R1


title: PM, IL4, RNA-Seq, replicate4


title: RB_29


title: 25-17T-H3K4me3-R1


title: 25-17N-H3K4me3-R1


title: PM, IL4, RNA-Seq, replicate3


title: RB_28


title: PM, IL4, RNA-Seq, replicate2


title: RB_27


title: 25-16T-H3K4me3-R1


title: 25-16T-H3K4me3-R2


title: PM, IL4, RNA-Seq, replicate1


title: WERI_48h_doxy_positive_biological_replicate_3

description:
MYCN knockdown model
ryl_et_al_MYCNKD_sleuth.txt

value: MYCNKD

value: doxycycline


title: WERI_48h_doxy_positive_biological_replicate_2


title: RB_25


title: 25-16N-H3K4me3-R1

value: Non-neoplastic


title: WERI_48h_doxy_positive_biological_replicate_1


title: PM, LPS+IFN-γ+ONX-0914, RNA-Seq, replicate4


title: RB_24

value: A


title: RB_30


title: 25-15T-H3K4me3-R2


title: 25-16N-H3K4me3-R2


title: 25-16T-H3K4me1-R1

value: H3K4me1 (Active Motif, #39297)


title: PM, LPS+IFN-γ+ONX-0914, RNA-Seq, replicate3


title: 25-17N-H3K4me3-R2


title: PM, LPS+IFN-γ+ONX-0914, RNA-Seq, replicate2


title: 25-15T-H3K4me3-R1


title: RB_23


title: WERI_48h_doxy_negative_biological_replicate_3

value: control


title: 25-15N-H3K4me3-R2


title: WERI_48h_doxy_negative_biological_replicate_2

value: retinoblastoma


title: PM, LPS+IFN-γ+ONX-0914, RNA-Seq, replicate1


title: RB_21


title: WERI_48h_doxy_negative_biological_replicate_1


title: 25-15N-H3K4me3-R1


title: RB_26


title: RB522_48h_doxy_positive_biological_replicate_3


title: PM, LPS+IFN-γ, RNA-Seq, replicate4

value: LPS+IFN-γ


title: RB_20


title: RB522_48h_doxy_positive_biological_replicate_2


title: PM, LPS+IFN-γ, RNA-Seq, replicate3


title: 25-14T-H3K4me3-R2


title: PM, LPS+IFN-γ, RNA-Seq, replicate1


title: 25-14N-H3K4me3-R2


title: 25-14T-H3K4me3-R1


title: PM, LPS+IFN-γ, RNA-Seq, replicate2


title: RB522_48h_doxy_positive_biological_replicate_1


title: RB522_48h_doxy_negative_biological_replicate_3


title: RB_12


title: RB_19


title: RB_13


title: 25-14N-H3K4me3-R1


title: PM, ONX-0914, RNA-Seq, replicate4


title: RB_22


title: RB522_48h_doxy_negative_biological_replicate_2


title: 25-13T-H3K4me3-R2


title: PM, ONX-0914, RNA-Seq, replicate3


title: RB_10


title: RB522_48h_doxy_negative_biological_replicate_1


title: RB_8


title: 25-13T-H3K4me3-R1


title: RB355_48h_doxy_positive_biological_replicate_1


title: 25-13N-H3K4me3-R2


title: PM, ONX-0914, RNA-Seq, replicate1


title: 25-13N-H3K4me3-R1


title: RB355_48h_doxy_positive_biological_replicate_3


title: RB_6


title: PM, RNA-Seq, replicate4

value: Control


title: RB355_48h_doxy_positive_biological_replicate_2


title: RB_5


title: 25-9-H3K27me3-R2

value: H3K27me3 (Active Motif, #39155)


title: PM, RNA-Seq, replicate2


title: PM, RNA-Seq, replicate3


title: RB_4

value: B


title: PM, RNA-Seq, replicate1


title: RB355_48h_doxy_negative_biological_replicate_1


title: 25-8-H3K27me3-R2


title: PM, ONX-0914, RNA-Seq, replicate2


title: 25-8-H3K27me3-R1


title: RB_7


title: 25-7-H3K27me3-R2


title: Batch3_PITX2

city: Muenster

first: Amer

last: Ghalawinji

address: Domagkstrasse 3

department: Institute of Human Genetics

institute: WWU

data_processing:
QC of raw reads using FastQC (v0.11.2)
Trimming read adapters using Trimmomatic (v0.36)
RNA-seq reads were mapped to ENSEMBL Homo_sapiens GRCh38 version 90 using STAR (v2.5.3a)
Read expression was quantified using StringTie (1.3.4d)
A differential expression analysis in R (v4.0.4) using DESeq2 R package (v1.30.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cell line of human induced pluripotent stem cells (hiPSC)

extract_protocol:
Total RNA was extracted from snap frozen aEHT using the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Atrial-like engineered heart tissue (aEHT) derived from hiPSC

tag: group

value: study sample

value: PITX2 Knockout


title: Batch2_PITX2


title: RB355_48h_doxy_negative_biological_replicate_2

last: Ketteler


title: Batch1_PITX2


title: AM, LPS+IFN-γ, CUT&TAG

data_processing:
The CUT&Tag data analysis began with the preprocessing of the raw sequencing reads, which involved the trimming of the data to eliminate low-quality sequences and adapters using Trimmomatic v0.39 with parameters “LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:20 MINLEN: 60”. Following this initial cleanup, the high-quality reads were mapped to the reference genome mm10 employing Bowtie2 v2.2.5. Subsequently, the BAM files were converted into BigWig format using deepTools v3.5.1 with CPM (counts per million) normalization, allowing for the quantification and visualization of NRF2 binding intensity across the genome.
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Following the steps outlined in the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illuminao) manual (Novoprotein Scientific, #N259-YH01), the experimental cells were extracted for the open chromatin regions associated with NRF2 binding, and then these regions were subjected to PCR amplification.
Sequencing libraries were prepared following the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illuminao) manual.

value: Lung

value: bronchoalveolar lavage macrophages

value: LPS+IFN-gamma


title: AM, LPS+IFN-γ+ONX0914, CUT&TAG


title: 25-7-H3K27me3-R1


title: AM, LPS+IFN-γ+ONX0914, ATAC

data_processing:
Raw sequence reads underwent quality evaluation using FastQC v0.11.9. Trimming of low-quality bases (<20) and removal of adapter sequences from raw reads was performed using Cutadapt v2.8 before alignment.Alignment to the mm10 reference genome was carried out using Bowtie2 v2.2.5 with the option "--very-sensitive". To ensure data integrity, duplicate sequences were removed using MarkDuplicates v3.0.0 implemented in Picard tools (http://broadinstitute.github.io/picard/). Additionally, sequences originating from mitochondria and blacklist regions were filtered out using Samtools v1.10 for ATAC-Seq data.
Assembly: GRCm38
Supplementary files format and content: bigWig

extract_protocol:
Fragmented DNA products were extracted using ATAC DNA Extract Beads. Amplified products were purified using ATAC DNA Clean Beads through a two-step sorting protocol (0.55×/1.2×).
For ATAC-seq, 100,000 cells were lysed in chilled Lysis Buffer, and sequencing libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711, Nanjing, China) following the manual protocol.


title: AM, LPS+IFN-γ, ATAC


title: Batch3_ERC01

value: control sample


title: 25-9-H3K27me3-R1

data_processing:
Raw ChIP-seq reads were aligned to hg19 genome by bwa (0.7.17).
Aligned reads were deduplicated and those with MAPQ>=10 were retained.
Narrow peaks (H3K27ac, H3K4me1, H3K4me3) were called by MACS2 (2.2.7.1) with q-value<=0.05. Board peaks (H3K27me3, H3K9me3) were called by Homer findPeaks in histone mode with p-value<=0.05.
Raw RNA-seq reads were trimmed by Trim Galore.
Trimmed RNA-seq reads were aligned to hg19 genome by STAR.
Assembly: hg19
Supplementary files format and content: bigwig track files (ChIP-seq)
Supplementary files format and content: txt gene read count files (RNA-seq)


title: RB_3


title: 25-6-H3K27me3-R1

value: Tumor


title: 25-6-H3K27me3-R2


title: RB355_48h_doxy_negative_biological_replicate_3

value: MYCNKD


title: edited_rep2

city: shanghai

first: Guoqiang

last: Zhou

address: Fudan University, Shanghai, 200438, China

institute: Fudan University School of Life Sciences

data_processing:
After trimming low-quality reads and removing sequencing adapters using trim_galore, the raw data was sorted using the "samtools sort" command. mtDNA coverage was assessed using "samtools depth", and mtDNA mutation analysis was performed using the MitoMutCall package. Chromatin accessibility information analysis was conducted using MACS2 for Peak calling. Differential expression peak analysis was performed using Diffbind. Transcriptome analysis involved alignment to a reference transcriptome using STAR, followed by differential expression analysis using DEseq2. Statistical analysis and plotting were carried out using R (version 4.3.1). We employed both base R plotting and ggplot2 for figure creation.
Assembly: hg38
Supplementary files format and content: Tab-separated values files

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum under standard conditions of 5% CO2 in a humidified atmosphere at 37 ℃.

extract_protocol: The OmicsCam enveloping the cells was treated with 100 μL of lysis buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (vol/vol) NP-40, and 1% (vol/vol) BSA, followed by incubation on ice for 5 minutes. Subsequently, 900 μL of washing buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 1% (vol/vol) BSA was added. After centrifugation at 1000g for 1 minute, the supernatant was removed, completing the mild lysis of the cells.

tag: cell line

value: Human embryonic kidney

value: mitochondrial ND4 gene-edited cell line


title: edited_rep3


title: wt_rep3

value: wild type


title: wt_rep1


title: edited_rep1


title: wt_rep2


title: Batch1_ERC01

value: control


title: 25-5-H3K27me3-R1

extract_protocol:
Nuclei extraction: Samples were shipped to Virginia Tech on dry ice and stored in liquid nitrogen vapor phase until use. Thin slices were cut from the tissue on dry ice with a sharp scalpel and transferred to the grinder (D9063, Sigma-Aldrich) pre-cooled on ice. Subsequent steps were performed on ice and centrifugation performed at 4°C. 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use] was added to the grinder. Tissue was homogenized by slowly douncing 20 times with pestle A and 30 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. Supernatant was removed and the crude nuclei pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by gently pipetting and then inverting the tube five times. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. The purified nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS).  MNase digestion of chromatin: Resuspended nuclei were counted and diluted to 4×10^6/ml if needed. 2 µl of PIC, 2 µl of 100 mM PMSF and 200 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added to 200 µl of nuclei suspension, mixed by vortexing and incubated at room temperature for 10 min. 20 µl of 100 mM CaCl2 and 5 µl of 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 44 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing chromatin fragments were transferred to a new 1.5 ml tube and placed on ice. 30 µl of chromatin solution was used for each ChIP assay (~50K nuclei).  Preparation of immunoprecipitation beads: 5 µl of protein A Dynabeads (10001D, Invitrogen) were used in each MOWChIP assay. The beads were washed twice with IP buffer (20 mM tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100) and resuspended in 150 µl of IP buffer. The following antibodies were used in this work: anti-H3K27ac (ab4729, Abcam), 0.125 µg/assay; anti-H3K4me1 (39297, Active Motif), 0.5 µl/assay; anti-H3K4me3 (ab8580, Abcam), 0.125 µg/assay; anti-H3K27me3 (39155, Active Motif), 0.5 µg/assay; anti-H3K9me3 (ab8898, Abcam), 0.125 µg/assay. The suspension was incubated on a rotator at 4°C overnight. The beads were washed with IP buffer twice and resuspended in 5 µl of IP buffer for loading in the MOWChIP device.  MOWChIP: The microfluidics based MOWChIP process, including device fabrication and operation, was performed following our published protocol (Zhu, B., Hsieh, YP., Murphy, T.W. et al. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 14, 3366–3394 (2019).).  RNA extraction: Tissue slices were placed in 200 µl of RNAlater-ICE frozen tissue transition solution (AM7030, Thermo Fisher Scientific) prechilled to -80°C. They were then incubated at -20°C overnight. Each RNA-seq library was prepared from 10ng RNA extracted from the tissue. Two technical replicates were prepared for each sample. Total RNA was extracted from the incubated tissue using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen).
ChIP-seq: Libraries were prepared using 2S Plus DNA library kit (IDT) following the manufacturer’s protocol. 1 × EvaGreen dye (Biotium) was added to the qPCR amplification mixture to monitor progress of amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library size distribution was examined using TapeStation (Agilent) and concentration was quantified with Kapa Library Quantification kit (Kapa Biosystems).  RNA-seq: Extracted total RNA was resuspended in 4.5 μL of RNase-free water with 5% RNase inhibitor (40 U/μL) added. 2 μL of oligo-dT primer (10 μM), 2 μL of dNTP mix (10 mM) and 4.3 μL of total RNA solution were mixed, incubated at 72°C for 3 minutes and immediately put on ice. Then 1 μL of SuperScript II reverse transcriptase (200 U/μL), 0.5μL of RNase inhibitor (40 U/μl), 4μL of Superscript II first-strand buffer, 1 μL of DTT (100 mM), 4 μL of 5 M Betaine, 0.12 μL of 1 M MgCl2, 0.2 μL of TSO (100 μM), 0.88 μL of nuclease-free water were added to the 8.3 μl mixture mentioned above. The reverse transcription (RT) reaction mix was then incubated at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, and lastly 70°C for 15 minutes. The RT reaction mix was mixed with 25 μL KAPA HiFi HotStart ReadyMix, 0.5 μL IS PCR primers (10 μM), 2.5 μL Evagreen dye, and 2 μL nuclease-free water, and amplified with: 98°C for 1 minute, 9–11 cycles of 98°C 15 seconds, 67°C 30 seconds, 72°C 6 minutes. The cDNA was purified using 30 μL of SPRIselect beads and eluted in 5 μL of low EDTA TE buffer. The RNA-seq library was made using tagmentation. 3 μL of home-made Tn5 was mixed with 3 μL of 50 μM pre-annealed P5/P7 transposon and incubated at 37°C for 1 hour. Assembled P5 and P7 transposons were then mixed well to form Tn5 mix. 1 μL cDNA (600 pg) and 1 μL of tagmentation buffer (TNP92110, Lucigen) were added to 8 μL Tn5 mix, and the mixture was incubated at 37°C for 1 hour. 1 μL of 10X stop buffer (TNP92110, Lucigen) was then added to the mixture to quench tagmentation. 11 μL SPRIselect beads were used to purify tagmented cDNA. The cDNA was then eluted in 9.5 μL of low EDTA TE buffer. 25 μL of KAPA HiFi HotStart ReadyMix was incubated at 98°C for 30 seconds, mixed with 9.5 μL tagmented cDNA and incubated at 72°C for 5 minutes. 1.5 μL of 100 μM P5 primer, 1.5 μL of 100 μM P7 primer, 10 μL nuclease-free water and 2.5 μL Evagreen were then added and amplified with: 98°C for 30 seconds; 10-12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 30 seconds. Amplified cDNA libraries were purified with 50 μL SPRIselect beads and eluted in 8 μL of low EDTA TE buffer. The RNA library preparation is adapted from Smart-Seq2 workflow (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014).)


title: Batch2_ERC01


title: BM, WT, scRNASeq

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

description:
10X Genomics
PW21001

data_processing:
Data were analyzed with a Cell Ranger pipeline.
Clustering cells, annotating cell clusters and analyzing differentially expressed genes were performed with Loupe Browser 5.0.1.
Bloodspot was used for annotating cell cluster.
Bioinformatics analyses were performed using the Reactome (https://reactome.org/).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Differential gene expression data

source_name: Bone marrow

extract_protocol:
HSCs/progenitors and B subsets (excluding mature B) were sorted and pooled together.In order to obtain an even coverage of each cell compartment/subset, we mixed approximately 1/6 of pre-B, ¼ of immature B (which are much more abundant than the others are) with all the HSCs/progenitors (including B progenitors).
GEX 3' whole transcriptome gene expression. Library was performed according to the manufactyer's instructions (single cell 3' v3 protocal, 10X Genomics)

treatment_protocol: Cre+ Ubxn3bf/f mice were treated with tamoxifen (TMX) (Ubxn3b-/-) or corn oil (Ubxn3b+/+) every two days for 4 doses. 30 days after the last dose of tamoxifen treatment,we collected bone marrow and pooled three mice per genotype.

value: Bone marrow

value: B cell

value: WT

value: Oil


title: BM, Ubxn3b KO,scRNAseq

description:
10X Genomics
PW21002

value: HSCs/progenitors and B subsets (excluding mature B)

value: Ubxn3b KO

value: Tamoxifen


title: APCTom_P3

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

data_processing:
After size selection and PCR enrichment, the RNA library was sequenced on Illumina platforms.  The sequencing data were aligned to a mouse reference genome (mm10) using Rsubread (version 2.4.3) 39. Raw counts were obtained from read alignments through refGene, and then further transferred into CPM by edgeR (version 3.32.1) 40. After filtering out low-expression genes with CPM lower than 10, differential expression was analyzed with the linear model using limma (version 3.46.0) 34. Genes with log2FC>1 and FDR<0.05 adjusted by B-H method were considered as significant differentially expressed genes (DEGs)
Assembly: mm10
Supplementary files format and content: align_fc.Rdata

source_name: Gonadal adipose tissue

extract_protocol:
Gonadal adipose tissue samples were subjected to direct mincing using a sharp scissor, followed by digestion in DMEM supplemented with 0.3 unit/ml Liberase TM (Roche) and 10% BSA at 37°C for 50 min with gentle shaking. After incubation, the resulting cell suspension was centrifuged at 400g for 3 min, and the supernatant was removed. The stromal vascular fractions (SVFs) present in the cell pellet were resuspended in DMEM and passed through 100 µm cell strainers. Subsequently, the red blood cells were lysed using RBC buffer for 5 min. The remaining cells were washed with PBS and resuspended in PBS containing 4% FBS and mouse FcR blocking reagent (MACS) at 4°C for 10 min, and further stained with anti-CD31antibodies and anti-CD45 antibody at 4°C for 30 min, washed and  passed through 70 µm cell strainers and then subjected to FACS SORP Aria (BD Biosciences) to sort out cells.The total RNA of sorted Tom+ and Tom- APCs from tumor bearing mice was extracted by using Single Cell RNA Purification Kit (NORGEN) according to the manufacturer’s instructions.
Total RNA were submitted to Novogene (China) and reverse transcribed into the cDNA library. Then the cDNA samples were fragmented, end-repaired, A-tailed, and ligated with adaptors.

value: Gonadal adipose tissue

value: Adipocyte progenitor cells

tag: sorted cells

value: tdTomato-positive